Especially since you cannot respec (end tree permanency)
Are you running the newest version? 0.9.5? Asking just in case, because in this last update respec through Story Points was added, some skills are marked as permanent and can't be unlearned but those are few.
Regarding everything else I agree quite a bit, I haven't found any explanation about what the general design philosophy behind the skill tree is. While the first three trees are generally (not entirely) cohesive in what they mean, industry seems like it doesn't know what it actually wants to make out of salvaged ships.
If red is "victory through weapons", green is "victory through strategy", blue is "victory through technology", then yellow should be "victory through money". And saving money is what's behind salvaging ships, skills regarding D-mods should be aimed towards either repairing them or making them substantially cheaper by being in that state (making d-mods less punishing is also cool). If we think that taking pieces out of a ships hyperdrive let it transverse jump (as explained by academy questline), then surely there are modifications that have minor impact on a ships performance yet make it more cost efficient.
Derelict contingent should instead let you apply unique d-mods that make a ships maintenance a percentage lower than what they are when in mint condition, you want to fly a bunch of space hot rods, not a zombie fleet that refuses to die for reasons beyond comprehension. In fact you might willfully take pieces out of a pristine ship just because your spacer nutcase of a captain doesn't want to take care of a paragon's marble columns and extinct jungalan leopard leather seats.
Tier 5 skills should be fun, being space Dr Frankenstein is fun I don't want colony management as tier 5 (ew)
Tl;dr: Space Hot Rods. Nuff said.